The second sentence expresses apparent impossibility or logical dubiousness.

It’s similar to the following:

Comment pouvez-vous croire qu’ils ont eu le temps de commettre un tel crime ?

Or, if not replying to anyone, it may be that you are dumbfounded, looking forward to an explaination.

Comment ont-ils bien pu avoir le temps de commetre un tel crime ?!

“Comment veux-tu” and “Comment voulez-vous” are often use to underline that the following statement is impossible. Basically you’re asking the person to find a way it could have happened, so they realize it can’t.

Kind of a similar idea to “How do you expect me to focus with all this noise ?!” (“Comment voulez-vous que je me concentre avec tout ce bruit ?!“)